Thats the same kind of problems I had with AROS, if I just want to edit with a tracker (milky, octamed or noisetrekkr) its fine, so long as I have a huge selection of samples, loops and instruments already loaded on the machine.
The problems come when you want to actually record new samples, vocals, guitars, drumloops, make new instruments or edit a sound already on the system beyond the trackers built in sample editor or instrument editor. I dumped stuff back and forth for a long time and finally just said forget it...
I still occasionally track demos on my aros box but once its a basic track, I have to use windows or linux to do the real work of making it a finished track.
I don't recommend any amigoid system for actual recording anything or editing samples/sound design work, or mastering but perhaps thats just been my experience.